university lille north of france LigASite database of binding sites
holo-structureHelp

PDB ID and HEADER, TITLE and COMPND records of the PDB file.

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1mb9
HYDROLASE HEADER
BETA-LACTAM SYNTHETASE COMPLEXED WITH ATP TITLE
BETA-LACTAM SYNTHETASE COMPND
Illustration of Binding SiteHelp

Figure showing the binding site residues. Ligands are displayed as CPK. Figures were drawn with Molscript (7) and rendered with Raster3D (8). PISA coordinates (3) are used when available (all entries except NMR). Ligands do not appear on the picture when PISA fails to apply symmetry operations to ligand coordinates.

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HETgroup - Residue ContactsHelp

List of binding site residues detected in this holo-structure.

Column 1 gives the position, coloured on a yellow-to-red scale depending on the number of holo-structures where the residue is in contact with a ligand.
Column 2 gives the identifier of the chain to which the residue belongs.
Column 3 gives the 3-letter amino acid code, coloured according to physico-chemical type.

The binding residues in this holo structure are listed for each ligand independently, following the ligand's unique ID.

Note that since PISA files are used whenever available, chain identifiers may differ from those in original PDB files.

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ATP B 701
247A VAL
248A LEU
249A SER
251A GLY
252A ILE
253A ASP
254A SER
271A VAL
272A SER
273A MET
280A GLU
326A TYR
329A PRO
330A LEU
333A LEU
346A THR
347A GLY
348A TYR
349A GLY
351A ASP
423A LYS
427A ARG
443A LYS
ATP H 702
247G VAL
248G LEU
249G SER
251G GLY
252G ILE
253G ASP
254G SER
271G VAL
272G SER
273G MET
280G GLU
326G TYR
329G PRO
330G LEU
333G LEU
346G THR
347G GLY
348G TYR
349G GLY
351G ASP
423G LYS
427G ARG
443G LYS
MG C 603
249A SER
251A GLY
280A GLU
443A LYS
MG I 602
249G SER
251G GLY
280G GLU
MG J 601
253G ASP
347G GLY
351G ASP
MG D 604
253A ASP
347A GLY
349A GLY
350A ALA
351A ASP
External LinksHelp

PDB The Protein Data Bank
CSA Catalytic Site Atlas
PDBSum Overview of the macromolecular structure
CATH Protein Structure Classification
Scop Structural Classification of Proteins
Pfam Protein Families and Domains
UniProt Universal Protein Resource

LIGPLOT (only on holo-pages) is hosted at the EBI.

The LigPlot Jmol links point directly to the Jmol visualisation interface provided on the PDBSum page.

Note that due to different software used, the atomic contacts of LigPlot and LigASite do not necessarily correspond.

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Links to external databases:

LigPlot (hosted at the EBI):

Download FilesHelp

Several files are provided for download:

• The XML file defining the residue-ligand contacts; this file contains data on the apo and all holo-structures.
• The XML Schema file defining the semantics of the XML file
• 3D coordinates of the structure used in constructing LigASite (PISA structure file whenever available, PDB file otherwise.
• 3D coordinates of the combined binding residues in the apo structure
• 3D coordinates of the binding residues of the holo structure (only on the holo page)

Coordinate files are in PDB format.

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Hide table of related structures
Help

List of related structure, containing both the apo-structure and other holo-structures.

Column 1 gives the PDB ID and column 2 the unique ID of the ligands (holo-structures only).

Clicking the blue 'Hide table of related structures' button removes the entire table.

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apo-structure
pdb ID
1m1z Details
other holo-structures
pdb ID Ligand Unique ID
1mbz GOLL_605 POPI_604 IOTH_603 _MGK_602 _MGJ_601 Details
GOLF_607 IOTB_606 _MGE_604 POPD_605 _MGC_603
POPI_604 IOTH_603 _MGK_602 _MGJ_601
1mc1 AMPH_705 PCXL_706 _MGI_602 POPJ_704 _MGK_605 Details
AMPB_702 POPC_701 _MGD_603 _MGE_601 PCXF_703
1jgt APCB_801 CMAA_803 _MGC_902 Details
APCE_802 _MGF_901 CMAD_804
Ligand ListHelp

Ligands present in this holo structure.

Column 1 shows the ligand HET code
Column 2 shows the name, chemical formula and (non-stereo) SMILES string.

Data in column 2 appears as 'not_found' when it is not present in the file 'pdb2smiles.xml' from www.rcsb.org.

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ATP NAME: ADENOSINE-5'-TRIPHOSPHATE
FORMULA: C10 H16 N5 O13 P3
SMILES: Nc1ncnc2[n](cnc12)C3OC(COP(O)(=O)OP(O)(=O)OP(O)(O)=O)C(O)C3O
MG NAME: MAGNESIUM ION
FORMULA: MG1
SMILES: [Mg++]
v9.7
April 2012
Interdisciplinary Research Institute, Computational Biology, Villeneuve d'Ascq, France
University College London, Biomolecular Structure and Modelling Unit, London, UK
Hospital for Sick Children and University of Toronto, Structural Biology and Biochemistry Program, Toronto, Canada
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